We present an improved result of lattice computation of the proton decay matrix elements in Nf=2+1 QCD. In this study, the significant improvement of statistical accuracy by adopting the error reduction technique of All-mode-averaging, is achieved for relevant form factor to proton (and also neutron) decay on the gauge ensemble of Nf=2+1 domain-wall fermions in mπ=0.34--0.69 GeV on 2.7~fm3 lattice as used in our previous work \cite{Aoki:2013yxa}. We improve total accuracy of matrix elements to 10--15\% from 30--40\% for p→πe+ or from 20--40\% for p→Kνˉ. The accuracy of the low energy constants α and β in the leading-order baryon chiral perturbation theory (BChPT) of proton decay are also improved. The relevant form factors of p→π estimated through the "direct" lattice calculation from three-point function appear to be 1.4 times smaller than those from the "indirect" method using BChPT with α and β. It turns out that the utilization of our result will provide a factor 2--3 larger proton partial lifetime than that obtained using BChPT. We also discuss the use of these parameters in a dark matter model.